MolNFT v1 · #82594 · protein

Vdr ligand binding domain in complex with 22S-butyl-2-methylidene-26, 27-dimethyl-19,24-dinor-1ALPHA,25-dihydroxyvitamin D3

3VRW · Vitamin D3 receptor: “Vdr ligand binding domain in complex with 22S-butyl-2-methylidene-26…”. X-ray diffraction, 1 ligand (YS5), 3 pockets (best druggability 0.87). MolNFT v1 #82594 on GenesisL1: 3D structure, binding sites and…

PDB: 3VRW
Type: protein
Length: 248 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vitamin D3 receptor; 13-meric peptide from mediator of RNA polymerase II transcription…
UniProt: P13053, Q15648
Ligands: YS5
Pockets: 3 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 67% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vitamin D3 receptor	protein	238	66% helix, 3% strand	P13053
C	13-meric peptide from mediator of RNA polymerase II transcription subunit 1	protein	10	70% helix, 0% strand	Q15648

Ligands and binding sites

YS5 · (1R,3R,7E,17beta)-17-[(2R,3S)-3-butyl-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	369	0.87	0.95	38	YS5
2	54	0.31	0.76	9	empty
3	58	0.27	0.73	19	empty

Interfaces

1 interface between chains.

A–C · 552 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3VRW · VDR ligand binding domain in complex with 22S-Butyl-2-methylidene-26,27-dimethyl-19,24-din… · the same entry in another collection · chain A against A, TM-score 1.00
P13053 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor (P13053) · a predicted model of the same protein · chain A against A, TM-score 0.98
Q15648 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain C against A, TM-score 0.78

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P13053
Every structure of UniProt Q15648
Elsewhere: RCSB PDB 3VRW · PDBe 3VRW · UniProt P13053 · UniProt Q15648

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